PROJECT SUMMARY/ABSTRACT Although numerous genetic loci have been associated with complex human disease through genome wide association studies (GWAS), further efforts are required to understand the mechanisms of association and thus disease risk. We need to understand how causal variation regulates expression of causal genes, and increasingly findings point to the interaction of cis- and trans-acting transcriptional mechanisms in this regard. These observations, and the apparent clustering of disease associated variation in transcriptional networks, have led us to study the transcription factors (TFs) associated with coronary artery disease (CAD), and in particular the bHLH factor TCF21. We have identified this TF, which is involved in vascular smooth muscle biology, as the causal gene at 6q23.2, and shown that it binds in target regions that are highly enriched among those identified by GWAS to be CAD associated, commonly in linkage disequilibrium with causal variants. This enrichment suggests that TCF21 mediates its effect on disease risk at least in part through regulation of expression of other CAD associated genes, and by inference these genes may also be involved in vascular wall related biology. TCF21 thus provides an exemplary model to explore cis- and trans-acting transcriptional interactions in highly relevant CAD loci. We thus propose our Central hypothesis: In CAD loci where the CAD causal variant (CCV) mediates TF binding, these TFs interact directly with TCF21 to regulate causal gene expression. In loci where the CCV is not located in a consensus TF binding motif, the causal variant indirectly regulates TCF21 binding and its mediated effects on chromatin structure and gene expression. In studies proposed here we aim to investigate in greater detail the mechanisms by which causal variation in CAD GWAS loci regulates TCF21 binding and gene expression. For CCVs located in TF binding motifs, studies in Aim 1 will determine whether the CCV related TFs regulate TCF21 binding by cooperative interaction or modulation of chromatin state or accessibility. In Aim 2, to study causal variants that do not reside in TF binding sites, we will map genome-wide quantitative trait variation that regulates TCF21 binding, H3K27Ac status, and chromatin accessibility. With these data, we will determine whether this type of disease variation indirectly mediates TCF21 binding through regulation of basic local chromatin availability. In Aim3 we will map chromosomal looping mediated by TCF21-DNA interactions with ChIA-PET, and use 3C to investigate the allelic effects of CCVs on these TCF21 mediated chromosomal structures in target CAD loci. Findings from these studies will vertically advance understanding of mechanisms by which causal variation mediates risk for CAD and other complex human diseases, bridging the gap between fundamental observations on regulatory variation and disease associations.